Same error in v. 2016.1. On Thu, Jul 13, 2017 at 2:39 PM, Alex <nedoma...@gmail.com> wrote:
> Here you are, as run on the production tpr: > > $ gmx make_ndx -f prod.tpr > GROMACS: gmx make_ndx, VERSION 5.0.5 > > ........ > ........ > > Reading structure file > Reading file prod.tpr, VERSION 5.0.5 (single precision) > Going to read 0 old index file(s) > Analysing residue names: > There are: 208 Other residues > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > > 0 System : 6537 atoms > 1 Other : 6537 atoms > 2 BUT : 84 atoms > 3 CBD : 53 atoms > 4 DEC : 6400 atoms > > > On Thu, Jul 13, 2017 at 2:35 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > >> What does gmx make_ndx think? >> >> Mark >> >> On Thu, Jul 13, 2017 at 10:34 PM Alex <nedoma...@gmail.com> wrote: >> >> > Hi Mark, >> > That's the problem: the names are exactly as they appear whenever atom >> > group selections are made... Any thoughts? >> > My topology is as clean as it gets: >> > >> > #include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/forcefield. >> itp" >> > #include "but.itp" >> > #include "cbd.itp" >> > #include "decane.itp" >> > >> > [ system ] >> > ; Name >> > >> > >> > [ molecules ] >> > ; Compound #mols >> > BUT 7 >> > CBD 1 >> > DEC 200 >> > >> > On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham <mark.j.abra...@gmail.com >> > >> > wrote: >> > >> > > Hi, >> > > >> > > As with any index group, you can make them with gmx make_ndx, gmx >> select, >> > > or your favourite text editor, and feed them to gmx grompp -n. You >> > normally >> > > get spoiled with automatically generated groups that happen to match >> > > moleculetypes and such. So probably you have SOL already. >> > > >> > > Mark >> > > >> > > On Thu, Jul 13, 2017 at 9:55 PM Alex <nedoma...@gmail.com> wrote: >> > > >> > > > Hi all, >> > > > >> > > > I have a system that a subsystem of interest (molecules BUT and CBD) >> > and >> > > > the solvent (DEC). I have simulated it and have a trajectory. >> > > > >> > > > I would like to find out the total energy of interaction between BUT >> > and >> > > > CBD as a function of simulated time, so my thought is to do -rerun >> and >> > > > exclude the interactions in the following group pairs: >> > > > >> > > > DEC-DEC >> > > > BUT-BUT >> > > > CBD-CBD >> > > > DEC-BUT >> > > > DEC-CBD >> > > > >> > > > When setting energygrp-excl with the following pairs, I immediately >> > get a >> > > > grompp error saying that DEC isn't an energy group. Since I've never >> > done >> > > > this before, can you please share your wisdom? >> > > > >> > > > Thank you, >> > > > >> > > > Alex >> > > > -- >> > > > Gromacs Users mailing list >> > > > >> > > > * Please search the archive at >> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > > > posting! >> > > > >> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > >> > > > * For (un)subscribe requests visit >> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >> > > > send a mail to gmx-users-requ...@gromacs.org. >> > > > >> > > -- >> > > Gromacs Users mailing list >> > > >> > > * Please search the archive at http://www.gromacs.org/ >> > > Support/Mailing_Lists/GMX-Users_List before posting! >> > > >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > >> > > * For (un)subscribe requests visit >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > > send a mail to gmx-users-requ...@gromacs.org. >> > > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
